Why are there more lincRNA genes than transcripts in Mus_musculus.GRCm38.100.gtf?

Question

[jennifer.conrad84]

Hi All,

There are 52446 annotated genes (ENSMUSG IDs) and 142,699 transcripts (ENSMUST IDs) in Mus_musculus.GRCm38.100.gtf. It makes sense that there are WAY more transcripts than genes. My question, however, is - why are there more genes than transcripts for lincRNA in the genome? Specifically there are 9847 genes and 8357 transcripts.

-Jen

[ATpoint]

How can there be a gene without a transcript? Some reproducible code available?

library(rtracklayer)

gtf <- import("http://ftp.ensembl.org/pub/release-100/gtf/mus_musculus/Mus_musculus.GRCm38.100.gtf.gz")

lincrna <- gtf[gtf$gene_biotype=="lincRNA"]

knitr::kable(data.frame(n_genes=length(unique(lincrna$gene_id)),
                        n_tx=length(unique(lincrna$transcript_id))))

| n_genes| n_tx|
|-------:|----:|
|    5629| 8358|

More tx than genes, as it biologically must be.

[jennifer.conrad84]

#STAR 
STAR --genomeDir star --readFilesCommand zcat --readFilesIn Rep2_Data/2_1.fq.gz Rep2_Data/2_2.fq.gz --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 --outSAMunmapped Within --twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM --runThreadN 16 --outFileNamePrefix Rep2_star_output/STAR_TP2/
#RSEM
RSEM-1.3.1/rsem-calculate-expression --bam -p 24 \
--paired-end --forward-prob .5 \
Rep2_star_output/STAR_TP2/Aligned.toTranscriptome.out.bam \
rsem/GRCm38 Rep2_rsem_output/RSEM_TP2/rsem >& \
Rep2_rsem_output/RSEM_TP2/rsem.log

[jennifer.conrad84]

To identify which biotypes are associated with each gene or transcript I ran the IDs through ensembl.org/biomart. Not sure if that is what is causing this....?

Answer 1

[JC]

why are there more genes than transcripts for lincRNA in the genome? Specifically there are 9847 genes and 8357 transcripts.

A gene contains one or more transcripts, for lincRNAs, there each lincRNA there is a gene record, and many have only 1 associated transcript